Published in Philos Trans R Soc Lond B Biol Sci on December 27, 2008
Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc Natl Acad Sci U S A (2010) 1.64
CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol (2010) 1.56
A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants. Philos Trans R Soc Lond B Biol Sci (2010) 1.33
Bayesian selection of nucleotide substitution models and their site assignments. Mol Biol Evol (2012) 1.12
Phylogenetic characterization of transport protein superfamilies: superiority of SuperfamilyTree programs over those based on multiple alignments. J Mol Microbiol Biotechnol (2012) 1.06
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Identification and function of a polyketide synthase gene responsible for 1,8-dihydroxynaphthalene-melanin pigment biosynthesis in Ascochyta rabiei. Curr Genet (2010) 0.89
Assessing parameter identifiability in phylogenetic models using data cloning. Syst Biol (2012) 0.87
Expansion of the APC superfamily of secondary carriers. Proteins (2014) 0.87
Benchmarking multi-rate codon models. PLoS One (2010) 0.84
Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences. PLoS One (2011) 0.82
Selective constraints on amino acids estimated by a mechanistic codon substitution model with multiple nucleotide changes. PLoS One (2011) 0.81
Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment. Curr Microbiol (2015) 0.78
Superiority of a mechanistic codon substitution model even for protein sequences in phylogenetic analysis. BMC Evol Biol (2013) 0.76
Detection of selection utilizing molecular phylogenetics: a possible approach. Genetica (2011) 0.75
Improved mitochondrial amino acid substitution models for metazoan evolutionary studies. BMC Evol Biol (2017) 0.75
Adaptive molecular evolution of MC1R gene reveals the evidence for positive diversifying selection in indigenous goat populations. Ecol Evol (2017) 0.75
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Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci U S A (1997) 5.76
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Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics (2003) 1.69
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A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proc Natl Acad Sci U S A (2006) 1.47
Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae). J Mol Evol (2001) 1.42
Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst Biol (2004) 1.16
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Evolution of the hymenopteran megaradiation. Mol Phylogenet Evol (2011) 4.76
Potential applications and pitfalls of Bayesian inference of phylogeny. Syst Biol (2002) 4.66
Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J (2007) 4.36
Southern hemisphere biogeography inferred by event-based models: plant versus animal patterns. Syst Biol (2004) 3.94
Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ Microbiol (2006) 3.44
An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat Genet (2005) 3.15
The hymenopteran tree of life: evidence from protein-coding genes and objectively aligned ribosomal data. PLoS One (2013) 3.14
Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics. Syst Biol (2008) 2.59
Inferring speciation and extinction rates under different sampling schemes. Mol Biol Evol (2011) 2.50
Performance-based selection of likelihood models for phylogeny estimation. Syst Biol (2003) 2.15
A new method for estimating the size of small populations from genetic mark-recapture data. Mol Ecol (2005) 2.09
Beneficial fitness effects are not exponential for two viruses. J Mol Evol (2008) 1.94
Testing the extreme value domain of attraction for distributions of beneficial fitness effects. Genetics (2007) 1.66
Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology (2007) 1.63
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
An enzymatic atavist revealed in dual pathways for water activation. PLoS Biol (2008) 1.52
High frequency of mutations that expand the host range of an RNA virus. Genetics (2007) 1.50
Mutational effects and population dynamics during viral adaptation challenge current models. Genetics (2010) 1.50
Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics (2002) 1.48
Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol Biol Evol (2005) 1.42
Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutation. J Theor Biol (2006) 1.38
A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution (2011) 1.35
Epistasis between beneficial mutations and the phenotype-to-fitness Map for a ssDNA virus. PLoS Genet (2011) 1.27
Skeletal morphology of Opius dissitus and Biosteres carbonarius (Hymenoptera: Braconidae), with a discussion of terminology. PLoS One (2012) 1.20
Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastids. Mol Biol Evol (2006) 1.09
Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation. Mol Biol Evol (2004) 1.09
Bayesian tests of topology hypotheses with an example from diving beetles. Syst Biol (2013) 1.05
The population biology of bacterial plasmids: a hidden Markov model approach. Genetics (2006) 1.05
A maximum-likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae): implications for insect phylogenetic studies. Mol Phylogenet Evol (2002) 1.04
Bayesian island biogeography in a continental setting: the Rand Flora case. Biol Lett (2010) 1.02
Evaluating the performance of likelihood methods for detecting population structure and migration. Mol Ecol (2004) 1.02
Estimation of selection intensity under overdominance by Bayesian methods. Stat Appl Genet Mol Biol (2009) 0.98
First-step mutations for adaptation at elevated temperature increase capsid stability in a virus. PLoS One (2011) 0.93
Convergent intron gains in hymenopteran elongation factor-1α. Mol Phylogenet Evol (2013) 0.92
Evolution of diversity in spatially structured Escherichia coli populations. Appl Environ Microbiol (2009) 0.89
Developing the electronic health record: what about patient safety? Health Serv Manage Res (2006) 0.88
Inference on the strength of balancing selection for epistatically interacting loci. Theor Popul Biol (2011) 0.87
Use of stochastic models to assess the effect of environmental factors on microbial growth. Appl Environ Microbiol (2005) 0.86
A Bayesian perspective on a non-parsimonious parsimony model. Syst Biol (2008) 0.86
Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation. Evolution (2011) 0.84
"Forms" of water mites (Acari: Hydrachnidia): intraspecific variation or valid species? Ecol Evol (2013) 0.83
Stickbreaking: a novel fitness landscape model that harbors epistasis and is consistent with commonly observed patterns of adaptive evolution. Genetics (2011) 0.82
As it happens: current directions in experimental evolution. Biol Lett (2012) 0.79
The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics. BMC Evol Biol (2013) 0.79
Empirical complexities in the genetic foundations of lethal mutagenesis. Genetics (2013) 0.77
Comments on 'Bayesian hierarchical error model for analysis of gene expression data'. Bioinformatics (2006) 0.75
Medical student attitudes towards complementary and alternative medicine (CAM) in medical education: a critical review. J Complement Integr Med (2016) 0.75
Inference for one-step beneficial mutations using next generation sequencing. Stat Appl Genet Mol Biol (2015) 0.75
Estimating the number of one-step beneficial mutations. Stat Appl Genet Mol Biol (2012) 0.75